It is a normal USB mouse:
http://www.logitech.com/repository/437/jpg/3221.1.0.jpg
And it is on a T60 notebook which has also a touchpoint and a touchpad.
All three input devices work (for moving and clicking).
While the Synaptics section was there IMO by default I would need it anyway as I
have there the option:
Option "TouchpadOff" "2"
to disable its tapping (but I no longer care as I no longer use the touchpad).

You're seeing a conflict between hotplugged input devices and the actual devices.
After the configured devices are created, all devices found by HAL are added.
These are added with the evdev driver, but without the mouse wheel option you
specified.
Furthermore, evdev grabs the device file, so any device added through hotplug
won't feed into /dev/input/mice (i.e. all mice).
There are two solutions to this:
- add "Option "AutoAddDevices" "off" to your ServerLayout. This deactivates
input device hotplugging and the mouse will use the options specified in the config.
- make evdev capable of ZAxisMapping options. I filed the bug for a
feature-request upstream. [1]
For now, the first option is better.
Closing as NOTABUG, since it was caused by a configuration problem.
[1] http://bugs.freedesktop.org/show_bug.cgi?id=16726

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